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Yup, I saw the warnings. That's why I made sure to export my databases so it wasn't a total disaster:-)

Since the translation to the new format is relatively simple (now that I've figured it out), maybe a web page with simple upgrade instructions and more detailed warnings could be set up? Something along the lines of

CAUTION: Upgrading will make previous databases unreadable without manulal intervention. See http://sqlite.perl.org for details.

I'll volunteer to write a draft of the web page if you think that's worthwhile.